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Depmap MetMap Drug Repurposing FireBrowse Cancer Cell Line Encyclopedia FireCloud Cancer Cell Line Factory Genome Data Analysis Center (GDAC) Project Achilles Gene Set Enrichment Analysis (GSEA) Connectivity Map Matrisome Project Clue Connectopedia Molecular Signatures Database (MSigDB) LINCS...

Reconstructing signaling pathways using regular language constrained paths

Publication: Journal Article

Wagner, Mitchell, Aditya Pratapa, and Murali. 2019. “Reconstructing Signaling Pathways Using Regular Language Constrained Paths”. Bioinformatics 35 (14): i624-i633.

CrossPlan: systematic planning of genetic crosses to validate mathematical models

Publication: Journal Article

Pratapa, Aditya, Neil Adames, Pavel Kraikivski, Nicholas Franzese, John Tyson, Jean Peccoud, and Murali. 2018. “CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models”. Bioinformatics 34 (13): 2237-44.

Algorithms for regulatory network inference and experiment planning in systems biology

Publication: Thesis

Pratapa, Aditya. 2020. “Algorithms for Regulatory Network Inference and Experiment Planning in Systems Biology”. Department of Computer Science.

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Published: "The ImageJ ecosystem: Open-source software for image visualization, processing, and analysis"

News: January 30, 2021

Protein Society journal Protein Science published a manuscript from co-PI Kevin Eliceiri's group highlighting the ImageJ codebase and community, including a review of the core features of the ImageJ ecosystem and how ImageJ has responded to imaging technology advancements with new plugins and tools...

Getting started using CellProfiler from the command line

Blog: April 30, 2021

Beth Cimini Cross posted from our GitHub wiki — check there for any future updates! Running CellProfiler from the command line has a major advantage — you don't need to spend computational power or memory creating the graphical user interface (GUI) that you're used to using in CellProfiler! It also...

Anne Carpenter featured in "Automating Drug Discovery With Machine Learning"

News: April 16, 2021

Technology Networks recently published "Automating Drug Discovery With Machine Learning" by Neeta Ratanghayra and featured a section on image-based profiling for drug discovery. COBA's Anne Carpenter was featured and spoke about image-based profiling in general as well as the use of machine learning...

CellProfiler Analyst 3.0 Release: Accessible data exploration and machine learning for image analysis.

Blog: April 28, 2021

David R. Stirling We have now released CellProfiler Analyst version 3.0! Download it here. As with CellProfiler 4, the primary goal of this release has been to migrate from Python 2 to Python 3 and modernise the application. We’ve also focused on improving performance and usability. Along with...

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Assistant to the Director Caitlin Ingelfinger +1 (617) 714-7350 trgoffice@broadinstitute.org Assistant to the Director Lee O'Neil trgoffice@broadinstitute.org Senior Laboratory Manager Maria Cecilia Saberi msaberi@broadinstitute.org Inquiries regarding open positions: TRGapplications@broadinstitute...